Microbiome Data Visualization
Do you know how to read
.qzafile?
## Reading and exploring Artifacts (.qza)
SVs <- read_qza(file = "data/feature_table.qza", tmp = "data/tmpdir", rm = TRUE)
SVs$data[1:4,1:4]
otu_table(q2_ps)[1:4,1:4]
## Reading metadata
read_q2metadata("data/sample_metadata.tsv")[1:5, 1:5]
read_tsv("data/sample_metadata.tsv", comment = "#q2:types", show_col_types = FALSE)[1:5, 1:5] %>%
rename(SampleID="#SampleID")
## Reading taxonomy
taxonomy<-read_qza("data/taxonomy.qza")
head(taxonomy$data)
## Parse tidy taxonomy only
taxonomy<-parse_taxonomy(taxonomy$data)
head(taxonomy)
Citation
Please consider citing the iMAP article[1] if you find any part of the IMAP practical user guides helpful in your microbiome data analysis.
References
[1]
Buza, T. M., Tonui, T., Stomeo, F., Tiambo, C.,
Katani, R., Schilling, M., … Kapur, V. (2019). iMAP: An integrated
bioinformatics and visualization pipeline for microbiome data analysis.
BMC Bioinformatics, 20. https://doi.org/10.1186/S12859-019-2965-4
Appendix
Project main tree
.
├── LICENSE
├── README.md
├── Shannon_by_time.pdf
├── Shannon_by_time.png
├── Shannon_by_time.svg
├── VennDiagram.2023-04-08_16-21-47.log
├── VennDiagram.2023-04-08_16-24-08.log
├── config
│  ├── config.yml
│  ├── pbs
│  │  ├── cluster.yaml
│  │  └── config.yaml
│  ├── samples.tsv
│  ├── slurm
│  │  ├── cluster.yaml
│  │  └── config.yaml
│  └── units.tsv
├── dags
│  ├── rulegraph.png
│  └── rulegraph.svg
├── data
│  ├── features.csv
│  ├── metadata.csv
│  ├── metadata.tsv
│  ├── q2_demo_ps.rds
│  ├── q2_ps.rds
│  ├── shannon.csv
│  └── taxonomy.csv
├── figures
│  ├── shannon_by_time.pdf
│  ├── shannon_by_time.png
│  ├── shannon_by_time.svg
│  ├── venn_metadata_shannon.pdf
│  ├── venn_metadata_shannon.png
│  └── venn_metadata_shannon.svg
├── images
│  ├── bkgd.png
│  ├── coders.png
│  ├── ml.png
│  ├── smkreport
│  │  └── screenshot.png
│  └── vizcover.png
├── imap-data-visualization.Rproj
├── index.Rmd
├── library
│  ├── apa.csl
│  ├── export.bib
│  ├── imap.bib
│  └── references.bib
├── report.html
├── resources
├── results
│  └── project_tree.txt
├── smk.css
├── styles.css
└── workflow
├── Snakefile
├── envs
│  ├── environment.yml
│  ├── mothur.yml
│  └── qiime220232.yml
├── report
│  ├── barplot.rst
│  ├── boxplots.rst
│  ├── hcluster.rst
│  ├── heatmaps.rst
│  ├── nmds.rst
│  ├── pcaordi.rst
│  ├── pcoaordi.rst
│  ├── scatter.rst
│  ├── shannon_metadata_venn.rst
│  ├── shannon_time_diversity.rst
│  └── workflow.rst
├── rules
│  ├── qiime2_viz.smk
│  ├── render_index.smk
│  ├── rmd_report.smk
│  └── rules_dag.smk
└── scripts
├── README.md
├── UntitledRMD.Rmd
├── common.R
├── convert_qiime2csv.R
├── import_qiime2_data.R
├── plot_shannon_diversity.R
├── plot_venn_metadata_shannon.R
├── qiime2R.R
├── qiime2_phyloseq_object.R
├── render.R
├── rules_dag.sh
├── smk_html_report.sh
└── tree.sh
16 directories, 76 filesUnlocking working directory.
Building DAG of jobs...
Creating report...
Adding venn_metadata_shannon.svg (0.17 MB).
Missing metadata for file figures/venn_metadata_shannon.svg. Maybe metadata was deleted or it was created using an older version of Snakemake. This is a non critical warning.
WorkflowError:
File figures/line_shannon_by_time.svg marked for report but does not exist.
[0408/175759.045573:ERROR:xattr.cc(63)] setxattr org.chromium.crashpad.database.initialized on file /var/folders/_6/mt8ts63j5c35k8kdk17yzq7h0000gn/T/: Operation not permitted (1)
[0408/175759.049329:ERROR:file_io.cc(91)] ReadExactly: expected 8, observed 0
[0408/175759.053703:ERROR:xattr.cc(63)] setxattr org.chromium.crashpad.database.initialized on file /var/folders/_6/mt8ts63j5c35k8kdk17yzq7h0000gn/T/: Operation not permitted (1)
[0408/175805.956533:INFO:headless_shell.cc(653)] Written to file /Users/tmbuza/Dropbox/MICROBIOME/imap-data-visualization/images/smkreport/screenshot.png.
Created 1 file(s):
/Users/tmbuza/Dropbox/MICROBIOME/imap-data-visualization/images/smkreport/screenshot.png
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